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- PDB-7qca: Spraguea lophii ribosome -

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Basic information

Entry
Database: PDB / ID: 7qca
TitleSpraguea lophii ribosome
Components
  • (40S ribosomal protein ...) x 23
  • (60S ribosomal protein ...) x 27
  • (Ribosomal protein ...) x 7
  • Guanine nucleotide binding protein beta subunit
  • RNA 23S
  • RNA 5S
  • RNA SSU
  • Ribosomal L29 protein
  • S60 ribosomal protein L10
  • Ubiquitin
  • Ubiquitin/40s ribosomal protein S27a fusion
  • eL14 LM0
  • eL37 LJJ
  • eS1 SB0
  • eS17 SR0
  • eS27 SBB
  • eS28 SCC
  • eS30 SEE
  • uL15 LAA
  • uS12 SX0
KeywordsRIBOSOME / Microsporidia
Function / homology
Function and homology information


preribosome / nonfunctional rRNA decay / preribosome, small subunit precursor / translational elongation / translational termination / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...preribosome / nonfunctional rRNA decay / preribosome, small subunit precursor / translational elongation / translational termination / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / maintenance of translational fidelity / rRNA processing / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / membrane / cytosol
Similarity search - Function
Ribosomal protein L32e, archaeal / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L22e ...Ribosomal protein L32e, archaeal / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L44e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S19e / : / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L6E / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein S7e / Ribosomal protein L30/YlxQ / Ribosomal protein S7e / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein L18e / : / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S8e / Ribosomal protein S5/S7, eukaryotic/archaeal
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S5 / 60S ribosomal protein L6 / 60S ribosomal protein L35a / Small ribosomal subunit protein uS11 / Ribosomal protein L15 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S5 / 60S ribosomal protein L6 / 60S ribosomal protein L35a / Small ribosomal subunit protein uS11 / Ribosomal protein L15 / Ribosomal protein L34 / 40S ribosomal protein S12 / 40S Ribosomal protein S19 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L26 / 40S ribosomal protein S9 / 60s ribosomal protein L21 / 40s ribosomal protein s24 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS2 / 60S ribosomal protein L7 / Large ribosomal subunit protein eL22 / 40S ribosomal protein S20 / 40S ribosomal protein S26 / Ubiquitin/40s ribosomal protein S27a fusion / Ribosomal protein S21E / 60S ribosomal protein L20 / 60S ribosomal protein L18 / 40S ribosomal protein S25 / 40S ribosomal protein S3 / 60S ribosomal protein L3 / 60S ribosomal protein L11 / S60 ribosomal protein L10 / 60S ribosomal protein L19 / Large ribosomal subunit protein uL4 / 60S ribosomal protein L17 / 40S ribosomal protein S16 / 60S ribosomal protein L36 / 60S ribosomal protein L3 / 60S ribosomal protein L23a / 40S ribosomal protein S4 / 40S ribosomal protein S8 / 60S ribosomal protein L5 / 40S ribosomal protein S18 / 40S ribosomal protein S29 / 40S ribosomal protein S15A / Large ribosomal subunit protein eL32 / Ribosomal protein S19 / 60S ribosomal protein L44 / Ribosomal protein L23 / 60S ribosomal protein L9 / Ubiquitin / Ribosomal protein L24E / 60S ribosomal protein L39 / 60S ribosomal protein L27 / 40S ribosomal protein S10 / 60S ribosomal protein L8 / Ribosomal protein L13A / 40S ribosomal protein S7 / Guanine nucleotide binding protein beta subunit / 60S ribosomal protein L13 / Uncharacterized protein / 40S ribosomal protein S13 / 60S ribosomal protein L31
Similarity search - Component
Biological speciesSpraguea lophii 42_110 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsGil Diez, P. / McLaren, M. / Isupov, M.N. / Daum, B. / Conners, R. / Williams, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust212439/Z/18/Z United Kingdom
CitationJournal: Nat Microbiol / Year: 2023
Title: CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state
Authors: McLaren, M. / Conners, R. / Isupov, M.N. / Gil-Diez, P. / Gambelli, L. / Gold, V.A.M. / Walter, A. / Connell, S.R. / Williams, B. / Daum, B.
History
DepositionNov 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_3d_fitting_list / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _refine.ls_d_res_high / _refine.ls_d_res_low
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L50: RNA 23S
L70: RNA 5S
LA0: 60S ribosomal protein L8
LAA: uL15 LAA
LB0: 60S ribosomal protein L3
LC0: 60S ribosomal protein L4
LCC: 60S ribosomal protein L3
LD0: 60S ribosomal protein L5
LDD: 60S ribosomal protein L31
LE0: 60S ribosomal protein L6
LEE: 60S ribosomal protein L32
LF0: 60S ribosomal protein L7
LFF: 60S ribosomal protein L35a
LG0: 60S ribosomal protein L8
LGG: Ribosomal protein L34
LH0: 60S ribosomal protein L9
LHH: Ribosomal L29 protein
LI0: S60 ribosomal protein L10
LII: 60S ribosomal protein L36
LJ0: 60S ribosomal protein L11
LJJ: eL37 LJJ
LL0: 60S ribosomal protein L13
LLL: 60S ribosomal protein L39
LM0: eL14 LM0
LMM: Ubiquitin
LN0: Ribosomal protein L15
LO0: Ribosomal protein L13A
LOO: 60S ribosomal protein L44
LP0: 60S ribosomal protein L17
LPP: 60S ribosomal protein L37a
LQ0: 60S ribosomal protein L18
LR0: 60S ribosomal protein L19
LS0: 60S ribosomal protein L20
LT0: 60s ribosomal protein L21
LU0: 60S ribosomal protein L22
LV0: Ribosomal protein L23
LW0: Ribosomal protein L24E
LX0: 60S ribosomal protein L23a
LY0: 60S ribosomal protein L26
LZ0: 60S ribosomal protein L27
S60: RNA SSU
SA0: 40S ribosomal protein S0
SAA: 40S ribosomal protein S26
SB0: eS1 SB0
SBB: eS27 SBB
SC0: 40S ribosomal protein S2
SCC: eS28 SCC
SD0: 40S ribosomal protein S3
SDD: 40S ribosomal protein S29
SE0: 40S ribosomal protein S4
SEE: eS30 SEE
SF0: 40S ribosomal protein S5
SFF: Ubiquitin/40s ribosomal protein S27a fusion
SG0: 40S ribosomal protein S6
SGG: Guanine nucleotide binding protein beta subunit
SH0: 40S ribosomal protein S7
SI0: 40S ribosomal protein S8
SJ0: 40S ribosomal protein S9
SK0: 40S ribosomal protein S10
SL0: 40S ribosomal protein S11
SM0: 40S ribosomal protein S12
SN0: 40S ribosomal protein S13
SO0: 40S ribosomal protein S14
SP0: Ribosomal protein S19
SQ0: 40S ribosomal protein S16
SR0: eS17 SR0
SS0: 40S ribosomal protein S18
ST0: 40S Ribosomal protein S19
SU0: 40S ribosomal protein S20
SV0: Ribosomal protein S21E
SW0: 40S ribosomal protein S15A
SX0: uS12 SX0
SY0: 40s ribosomal protein s24
SZ0: 40S ribosomal protein S25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,642,117442
Polymers2,629,85974
Non-polymers12,258368
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules L50L70S60

#1: RNA chain RNA 23S


Mass: 849039.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Production host: Spraguea lophii (fungus)
#2: RNA chain RNA 5S


Mass: 38356.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Production host: Spraguea lophii (fungus)
#41: RNA chain RNA SSU


Mass: 444812.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Production host: Spraguea lophii (fungus)

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60S ribosomal protein ... , 27 types, 27 molecules LA0LB0LC0LCCLD0LDDLE0LEELF0LFFLG0LH0LIILJ0LL0LLLLOOLP0LPPLQ0LR0LS0LT0LU0LX0LY0LZ0

#3: Protein 60S ribosomal protein L8


Mass: 27005.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_78 / Production host: Spraguea lophii (fungus)
#5: Protein 60S ribosomal protein L3


Mass: 44320.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_68 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XFB1
#6: Protein 60S ribosomal protein L4


Mass: 37241.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_73 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WCM8
#7: Protein 60S ribosomal protein L3


Mass: 12484.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_69 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WAY0
#8: Protein 60S ribosomal protein L5


Mass: 33892.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_75 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XIG7
#9: Protein 60S ribosomal protein L31


Mass: 12854.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2196 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XW48
#10: Protein 60S ribosomal protein L6


Mass: 20220.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2210 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W5S3
#11: Protein 60S ribosomal protein L32


Mass: 16075.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_70 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XKE0
#12: Protein 60S ribosomal protein L7


Mass: 27935.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_76 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W946
#13: Protein 60S ribosomal protein L35a


Mass: 12757.991 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_71 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W662
#14: Protein 60S ribosomal protein L8


Mass: 23604.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_77 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XU63
#16: Protein 60S ribosomal protein L9


Mass: 21538.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_79 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XRZ9
#19: Protein 60S ribosomal protein L36


Mass: 11350.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_72 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WED1
#20: Protein 60S ribosomal protein L11


Mass: 19484.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_56 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WB69
#22: Protein 60S ribosomal protein L13


Mass: 19513.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_32 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XVM9
#23: Protein 60S ribosomal protein L39


Mass: 6227.581 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2202 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XTP1
#28: Protein 60S ribosomal protein L44


Mass: 11990.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_74 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XL20
#29: Protein 60S ribosomal protein L17


Mass: 19114.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_58 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WDR4
#30: Protein 60S ribosomal protein L37a


Mass: 10151.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2590 / Production host: Spraguea lophii (fungus)
#31: Protein 60S ribosomal protein L18


Mass: 21378.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_59 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WAI2
#32: Protein 60S ribosomal protein L19


Mass: 19549.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_60 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WBY9
#33: Protein 60S ribosomal protein L20


Mass: 20043.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_61 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WAG4
#34: Protein 60s ribosomal protein L21


Mass: 18344.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_62 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W8F6
#35: Protein 60S ribosomal protein L22


Mass: 12854.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_63 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W958
#38: Protein 60S ribosomal protein L23a


Mass: 12557.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_64 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XFW8
#39: Protein 60S ribosomal protein L26


Mass: 15026.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_65 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W884
#40: Protein 60S ribosomal protein L27


Mass: 18247.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_66 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XU08

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Protein , 14 types, 14 molecules LAALHHLI0LJJLM0LMMSB0SBBSCCSEESFFSGGSR0SX0

#4: Protein uL15 LAA


Mass: 16609.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Production host: Spraguea lophii (fungus)
#17: Protein Ribosomal L29 protein


Mass: 14183.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2194 / Production host: Spraguea lophii (fungus)
#18: Protein S60 ribosomal protein L10


Mass: 25142.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1601 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WBF8
#21: Protein eL37 LJJ


Mass: 10517.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Production host: Spraguea lophii (fungus)
#24: Protein eL14 LM0


Mass: 14158.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1179 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XVN9
#25: Protein Ubiquitin


Mass: 14563.868 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2019 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XSQ3
#44: Protein eS1 SB0


Mass: 25934.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Production host: Spraguea lophii (fungus)
#45: Protein eS27 SBB


Mass: 9189.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Production host: Spraguea lophii (fungus)
#47: Protein eS28 SCC


Mass: 7288.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Production host: Spraguea lophii (fungus)
#51: Protein eS30 SEE


Mass: 6816.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Production host: Spraguea lophii (fungus)
#53: Protein Ubiquitin/40s ribosomal protein S27a fusion


Mass: 16937.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2039 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W9X5
#55: Protein Guanine nucleotide binding protein beta subunit


Mass: 36182.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2232 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XVG3
#66: Protein eS17 SR0


Mass: 14055.251 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Production host: Spraguea lophii (fungus)
#72: Protein uS12 SX0


Mass: 15822.722 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Production host: Spraguea lophii (fungus)

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Ribosomal protein ... , 7 types, 7 molecules LGGLN0LO0LV0LW0SP0SV0

#15: Protein Ribosomal protein L34


Mass: 12020.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1567 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W7C6
#26: Protein Ribosomal protein L15


Mass: 24200.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1565 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W7A2
#27: Protein Ribosomal protein L13A


Mass: 22885.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1564 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XUD8
#36: Protein Ribosomal protein L23


Mass: 15239.987 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2233 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XLC4
#37: Protein Ribosomal protein L24E


Mass: 15342.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1566 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XSY2
#64: Protein Ribosomal protein S19


Mass: 18514.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1570 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XKY9
#70: Protein Ribosomal protein S21E


Mass: 7768.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2726 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WAC1

+
40S ribosomal protein ... , 23 types, 23 molecules SA0SAASC0SD0SDDSE0SF0SG0SH0SI0SJ0SK0SL0SM0SN0SO0SQ0SS0ST0SU0SW0SY0SZ0

#42: Protein 40S ribosomal protein S0


Mass: 26201.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_25 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W8R1
#43: Protein 40S ribosomal protein S26


Mass: 11974.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1572 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W9M7
#46: Protein 40S ribosomal protein S2


Mass: 27241.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2189 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W7R5
#48: Protein 40S ribosomal protein S3


Mass: 27516.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_40 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WAW0
#49: Protein 40S ribosomal protein S29


Mass: 7891.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2174 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XJB1
#50: Protein 40S ribosomal protein S4


Mass: 31442.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_43 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XG51
#52: Protein 40S ribosomal protein S5


Mass: 21982.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_44 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W4M9
#54: Protein 40S ribosomal protein S6


Mass: 26238.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_45 / Production host: Spraguea lophii (fungus)
#56: Protein 40S ribosomal protein S7


Mass: 19132.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_46 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XV29
#57: Protein 40S ribosomal protein S8


Mass: 19912.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_47 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XGW2
#58: Protein 40S ribosomal protein S9


Mass: 21365.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_48 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W8E3
#59: Protein 40S ribosomal protein S10


Mass: 12702.538 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_26 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XU48
#60: Protein 40S ribosomal protein S11


Mass: 18109.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_27 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W8R0
#61: Protein 40S ribosomal protein S12


Mass: 14343.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_28 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W7D2
#62: Protein 40S ribosomal protein S13


Mass: 16191.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_29 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XVZ9
#63: Protein 40S ribosomal protein S14


Mass: 14708.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_30 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W6I0
#65: Protein 40S ribosomal protein S16


Mass: 16415.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_2103 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WDU9
#67: Protein 40S ribosomal protein S18


Mass: 18171.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_33 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XJA1
#68: Protein 40S Ribosomal protein S19


Mass: 16603.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_34 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W7P5
#69: Protein 40S ribosomal protein S20


Mass: 13777.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_35 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W986
#71: Protein 40S ribosomal protein S15A


Mass: 14620.056 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_31 / Production host: Spraguea lophii (fungus) / References: UniProt: S7XK92
#73: Protein 40s ribosomal protein s24


Mass: 17189.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_37 / Production host: Spraguea lophii (fungus) / References: UniProt: S7W8J5
#74: Protein 40S ribosomal protein S25


Mass: 14777.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spraguea lophii 42_110 (fungus) / Strain: 42_110 / Gene: SLOPH_1571 / Production host: Spraguea lophii (fungus) / References: UniProt: S7WAV8

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Non-polymers , 3 types, 368 molecules

#75: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 199 / Source method: obtained synthetically / Formula: K
#76: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 160 / Source method: obtained synthetically / Formula: Mg
#77: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Ribosome / Type: RIBOSOME / Entity ID: #1-#74 / Source: NATURAL
Source (natural)Organism: Spraguea lophii 42_110 (fungus)
Buffer solutionpH: 7.5
Details: Solution with HEPES, Potassium Acetate and Magnesium acetate was autoclaved. DTT was added fresh just before sample preparation.
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2100 mMPotassium AcetateCH3CO2K1
31 mMDithiothreitolDTT1
415 mMMagnessium AcetateMg(C2H3O2)21
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monomeric ribosomes from Spraguea lophii
Specimen supportDetails: 20 mA. Carbon coated grid / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288.15 K / Details: blot force -1 and blot time 4 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Specimen-ID: 1

IDAccelerating voltage (kV)Model
1300TFS KRIOS
2200TFS TALOS
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1141.5GATAN K3 BIOQUANTUM (6k x 4k)
2241.34GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
EM software
IDNameVersionCategoryImaging-ID
2EPUimage acquisition1
4Warp1.09CTF correction
7Cootmodel fitting
9UCSF Chimeramodel fitting
10UCSF ChimeraXmodel fitting
11MOLREPmodel fitting
12REFMACmodel refinement
14RELION3.1initial Euler assignment
15RELION3.1final Euler assignment
16RELION3.1classification
17RELION3.13D reconstruction
30EPUimage acquisition2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 977879
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 285940 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingPDB-ID: 6RM3

6rm3


Accession code: 6RM3 / Source name: PDB / Type: experimental model
RefinementResolution: 2.79→2.79 Å / Cor.coef. Fo:Fc: 0.877 / WRfactor Rwork: 0.256 / SU B: 9.074 / SU ML: 0.169 / Average fsc overall: 0.8886 / Average fsc work: 0.8886 / ESU R: 0.168 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rwork0.2561 3740202 -
all0.256 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 79.767 Å2
Baniso -1Baniso -2Baniso -3
1--0.139 Å20.139 Å20.036 Å2
2---0.25 Å2-0.102 Å2
3---0.389 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.011182727
ELECTRON MICROSCOPYr_angle_refined_deg1.8321.758265020
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.116510555
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.39821.3344475
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.4071517796
ELECTRON MICROSCOPYr_dihedral_angle_4_deg18.69115729
ELECTRON MICROSCOPYr_chiral_restr0.1630.231079
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.02104414
ELECTRON MICROSCOPYr_nbd_refined0.1840.284948
ELECTRON MICROSCOPYr_nbtor_refined0.2890.2227528
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.10.23066
ELECTRON MICROSCOPYr_metal_ion_refined0.0760.224
ELECTRON MICROSCOPYr_mcbond_it6.4459.27842442
ELECTRON MICROSCOPYr_mcangle_it11.1113.90452923
ELECTRON MICROSCOPYr_scbond_it6.3737.227140285
ELECTRON MICROSCOPYr_scangle_it10.33610.538212097
ELECTRON MICROSCOPYr_lrange_it22.782131.401734220
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.78-2.8520.4362768140.4362768140.7150.436
2.852-2.9310.4082704850.4082704850.7540.408
2.931-3.0150.3762617640.3762617640.7980.376
3.015-3.1080.342547710.342547710.840.34
3.108-3.210.3022473610.3022473610.8770.302
3.21-3.3230.2662385620.2662385620.9070.266
3.323-3.4480.2412304560.2412304560.9250.241
3.448-3.5890.232219300.232219300.9330.23
3.589-3.7490.2262125620.2262125620.9360.226
3.749-3.9320.222033900.222033900.9420.22
3.932-4.1440.2151933740.2151933740.9480.215
4.144-4.3960.2121822970.2121822970.9530.212
4.396-4.6990.2091718310.2091718310.9580.209
4.699-5.0750.2011601070.2011601070.960.201
5.075-5.560.21470780.21470780.9550.2
5.56-6.2160.2111329820.2111329820.9450.211
6.216-7.1770.2351173100.2351173100.930.235
7.177-8.7890.243988280.243988280.9280.243
8.789-12.4250.243764770.243764770.940.243
12.425-337.280.369418230.369418230.960.369

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